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Table 1 Individual chromosomal islands of up- or down-regulation.

From: A genome-wide map of aberrantly expressed chromosomal islands in colorectal cancer

expression change start region end region start gene end gene potential tumor genes, hereditary CRC, known chromosomal imbalances
loss 1p36.33 1p36.32 TNFRSF18 ARHGEF16 amplification of 1p36.33-p32 in CRC [25] // deletion of 13p36.3 in 25% of neuroblastomas and 87% of cell lines [45] // loss of expression and genomic deletion on 1p [17]
loss 1p36.13 1p36.11 PADI1 DKFZP434L0117 E2F2 // ID3 // loss of 1p36.1 in CRC [22, 25] // loss of expression and genomic deletion on 1p [17]
loss 1p35.1 1p34.3 HDAC1 PSMB2 LCK at 1p35.1 // hereditary CRC at 1p35 (OMIM 114500) // loss of expression and genomic deletion on 1p [17]
gain 1q32.1 1q41 PIGR DKFZp547M236 1q32 amplification involving MDM4 and CNTN2 in malignant gliomas [46]
gain 2p25.3 2p24.2 Hs.8379.0 VSNL1 hereditary CRC at 2p25 (OMIM 114500)
loss 2p11.2 2q12.1 MAT2A MGC11332 83% loss of 2p11 in mantle cell lymphoma [47] // loss in mantle cell lymphoma [48]
gain 2q31.3 2q32.2 SSFA2 NAB1 hereditary HNPCC3 at 22q31-q33 (OMIM 600258) // familial breast cancer at 2q (OMIM 114480)
gain 2q33.2 2q35 Hs.163603 AAMP familial breast cancer at 2q (OMIM 114480)
loss 2q37.3 2q37.3 SCLY FARP2 familial breast cancer at 2q (OMIM 114480)
gain 3p25.3 3p25.1 KIAA0121 CAPN7 amplification of 3p25.2 in CRC [25] // RAF1 at 3p25.2 // FBLN1 at 3p25.2
gain 3p25.1 3p24.2 RAFTLIN THRB  
gain 3p24.2 3p23 FLJ20604 CLASP2  
loss 3p21.31 3p21.31 CELSR3 NPR2L hereditary HNPCC2 at 3p21.3 (OMIM 609310) // RASFF1
gain 3p11.1 3q13.11 MGC26717 ALCAM frequent 3q11.2-q13.1 amplifications in cervix carcinomas [49]
loss 3q13.13 3q21.2 Hs.23762.0 ITGB5  
loss 4p15.32 4p14 LAP3 Hs.118993 deletions of 4p14 in CRC [24] // SLIT2 at 4p15 is inactivated by hypermethylation in gliomas [33] // SLIT2 suppresses tumor growth [32] // loss of expression and genomic deletion on 1p [17]
loss 4q13.2 4q13.3 YT521 CXCL6 global loss of expression and genomic deletion on 4 [17]
loss 4q21.21 4q22.3 PRKG2 LIM transition of follicular B cell lymphoma to diffuse large cell lymphoma accompanied by 4q21-q23 deletions // global loss of expression and genomic deletion on 4 [17]
loss 4q34.1 4q35.2 HPGD Hs.130535 deletion of 4q34-q35 in colorectal cancer cell lines [25] // CASP3 at 4q34.3 // global loss of expression and genomic deletion on 4 [17]
loss 5q15 5q23.2 Hs.444378 Hs.97104 hereditary colorectal adenoma and carcinoma 1 (CRAC1) (OMIM 601228) at 15q15.3-q221 // APC at 5q21 // loss of expression and genomic deletion on 5q [17]
gain 5q31.1 5q31.3 HTGN29 Hs.443121 loss of expression and genomic deletion on 5q [17]
loss 5q31.3 5q33.1 NDFIP1 FLJ10290 amplification of 5q32-q34 in prostate cancer [50] // PDGFRB at 5q32 // loss of expression and genomic deletion on 5q [17]
gain 5q33.2 5q35.1 MRPL22 FBXW1B amplification of 5q32-q34 in prostate cancer [50] // loss of expression and genomic deletion on 5q [17]
gain 6p25.3 6p24.2 DUSP22 NEDD9 amplification of 6p25 in 24% of mantle cell lymphomas [47] // amplification of 6p25 in 75% of prostate cancers [51]
loss 6p22.3 6p22.2 CAP2 SLC17A4 most frequent amplification of 6p22.3 in bladder cancer arrayCGH study [52]
loss 6p21.32 6p21.32 PBX2 RAB2L  
gain 6p21.31 6p21.2 HMGA1 RNF8 CDKN1A at 6p21.2 // PIM1 at 6p21.2
gain 6q23.3 6q24.2 DUFD1 Hs.12565 amplification of 6q23-q24 assosicated with short survival [22]
gain 7p22.3 7p21.3 FLJ23471 ICA1 hereditary HNPCC4 at 7p22 (gene PMS2) // gain of expression and genomic amplification of 7 [17]
gain 7p21.2 7p15.3 ETV1 OSBPL3 amplification of 7p21 in mantle cell lymphomas [47] // amplification of 7p21 in osteosarcoma [53] // gain of expression and genomic amplification of 7 [17]
gain 7p14.3 7p13 LSM5 NPC1L1 gain of expression and genomic amplification of 7 [17]
loss 7q11.23 7q21.3 SRCRB4D CAS1 amplification of 7q11.1-q12 in metastatic CRC [24] // gain of expression and genomic amplification of 7 [17]
gain 7q31.31 7q33 FAM3C MGC5242 prostate cancer aggressiveness linked to 7q32-q33 [54] // gain of expression and genomic amplification of 7 [17]
gain 8q11.23 8q21.11 ATP6V1H ANKTM1 amplifications of 8q11-q24 in metastasing CRC [29] // LYN at 8q12.1 // MOS at 8q12.1 // familial breast cancer at 8q11 (OMIM 114480) // amplifications at 8q in CRC [18, 21, 23, 25] // gain of expression and genomic amplification of 8q [17]
gain 8q22.3 8q24.22 TIEG SLA amplifications of 8q11-q24 in metastasing CRC [29] // MYC at 8q24.21 // PVT1 at 8q24.21 // amplification of 8q23-q24 in prostate cancer [55]// gain of expression and genomic amplification of 8q [17]
loss 9p21.3 9p21.1 IFNA4 SMU-1 loss of 9p21 in CRC [25] // TUBE1 at 9p21 // CDKN2A alias p16INK4A at ??? // frequent deletion of 9p21 in prostate cancer [56] // deletion of 9p21.3 in bladder cancer [57]
loss 9p13.3 9p13.3 BAG1 OPRS1 frequent LOH at 9p13-p21 in melanoma [58]
loss 9q21.11 9q21.32 Hs.173519.0 Hs.522256 loss of 9q21-q22 in mantle cell lymphoma [59]
loss 9q34.11 9q34.11 FLJ14596 GPR107 ABL1 protooncogene at 9q34.12
loss 10p15.3 10p12.2 Hs.255096 Hs.57079.0 frequent LOH of 10p15 in gastric cancer [60] // telomerase repressor at 10q15.1 [61] // deletion of 10p14 in mantle cell lymphoma [47, 59] // OPTN at 10p14 [62]
loss 10q11.21 10q11.23 Hs.173866.0 MOB RET at 10q11.21 // LOH in prostate cancer at 10q11.21 [51]
loss 11p15.5 11p15.5 RNH MUC5AC hereditary CRC at 11p15.5 / HRAS at 11p15.5 // 11p15.5 methylation-dependent expression silencing and imprinting in phaeochromocytomas [63]
gain 11p15.5 11p15.4 CTSD SSA1 CTSD (Cathepsin D) at 11p15.5 // familial breast cancer at 11p15.5 (OMIM 114480)
gain 11p13 11p12 Hs.120054.0 TRAF6 WT1 at 11p13
gain 11p11.2 11q12.1 ch-TOG CTNND1  
loss 11q13.2 11q13.4 LOC338692 SKD3 BCL1 at 11q13.3 (anti-apoptotic, amplified in breast cancer) // CCND1 at 11q13.3 (amplified in breast cancer [64]) // FGF3 at 11q13
gain 11q14.1 11q21 Hs.26339.0 MTMR2  
loss 11q23.3 11q23.3 AMICA HYOU1 frequent loss of 11q23.3-q25 in neuroblastoma [65] // loss of 11q23 in 33% of 73 tumor types [66]
loss 12p13.31 12p13.2 TPI1 CLEC1 CDKN1B (alias p27Kip1) at 12p13.2
loss 12p12.3 12q12 CGI-26 MADP-1 familial breast cancer at 12p12.1 (OMIM 114480)
gain 12q14.2 12q22 Hs.132260.0 Hs.403150 MDM2 at 12q15 // validated up-regulation of GPR49 at 12q21.1
gain 12q22 12q23.3 USP44 KIAA1033  
loss 12q23.3 12q24.11 SART3 Hs.18370.0 loss of 12q24 in pancreas tumors [55]
gain 13q14.11 13q22.1 LOC283508 PIBF1 RB1 at 13q14.2 // ARLT1 at 13q14 // gain of expression and genomic amplification of 13q [17]
gain 14q22.1 14q22.2 PSMC6 AND-1 14q22-q23 losses in 25% of tumor types [66]
loss 14q24.1 14q24.3 Hs.369329 Hs.169812 hereditary CRC at 14q24.3 (OMIM 114500) // loss of 14q24-31 in CRC metastases [36] // FOS at 14q24.3 // hereditary HNPCC7 at 14q24.3 (gene MLH3) (OMIM) // poor prognosis when 14q24-q31 is lost in renal cell carcinoma [67] // loss of expression and genomic DNA of 14q [17]
loss 14q32.33 14q32.33 ZFYVE21 Hs.248015.0 14q32 is a tumor suppressive region in esophagal cancer [68] // loss of expression and genomic DNA of 14q [17]
loss 15q21.1 15q22.31 FBN1 CLPX association between loss of 15q21.1-q22.2 and survival in hepatocellular carcinoma [69] // allelic imbalance at 15q21.1 in breast cancer metastases [70] // loss of expression and genomic DNA of 15q [17]
loss 15q26.1 15q26.3 GABARAPL3 FLJ25222 loss of expression and genomic DNA of 15q [17]
loss 16p12.1 16p11.2 GTF3C1 PRSS8  
loss 16q12.1 16q13 TRF4-2 FLJ13154  
gain 16q22.1 16q22.2 PSMB10 KIAA0931 CDH1 (E-Cadherin) at 16q22.1
loss 17p13.3 17p13.2 RPA1 DHX33 loss of 17p13.2 in CRC [25] // DHX33 at 17p13.2
loss 17p13.1 17p11.2 GAS7 COPS3 Near TP53 at 17p13.1 .// hereditary CRC at 17p11.2 (OMIM 114500) // hereditary CRC at 17p13.1 (OMIM 114500) // // familial breast cancer at 17p13 (OMIM 114480) // loss of 17p12 in CRC [25] // ELAC2 at 17p11.2
gain 17q21.33 17q23.2 TOB1 PPM1D NME1 (NME23) at 17q21.33 // familial breast cancer at 17q22-q23 (OMIM 114480) //
loss 18p11.21 18q12.1 MGC24180 DSC3 loss of expression and genomic DNA of 18 [17]
loss 18q21.1 18q23 CGBP MBP DCC at 18q21.3 (OMIM 120470) // loss of 18q21.1 in CRC cell lines [25] // SMAD2 // SMAD4 mutations in CRC [71] // loss of expression and genomic DNA of 18 [17]
loss 19p13.3 19p13.3 DF APCL  
gain 19p13.2 19p13.12 FLJ20244 NOTCH3  
gain 19p13.11 19q13.12 LOC114977 TYROBP NIFIE14 at 19q13.12
loss 19q13.2 19q13.32 MGC20255 TOMM40 AKT2 (breast carcinoma at 19q13.2 // TGFB1 at 19q13.2 // proapototic Bax at 19q13.33
gain 20p11.21 20q11.21 C1QR1 BCL2L1  
gain 20q11.22 20q11.23 RNPC2 C20orf102 SRC at 20q11.23 (overexpressed in breast carcinoma) // gain of expression and genomic DNA of 20q [17]
gain 20q13.12 20q13.33 SLC12A5 ARFRP1 gain of expression and genomic DNA of 20q [17]
gain 21q22.12 21q22.3 C21orf18 TMPRSS2 ETS2 at 21q22.2
loss 21q22.3 21q22.3 PFKL COL6A1 COL18A1 (Endostatin) at 21q22.3
loss 22q11.21 22q12.1 SDF2L1 TPST2 familial breast cancer at 22q12.1 (OMIM 114480)
loss 22q13.31 22q13.33 Hs.296370.0 RABL2B hereditary CRC at 22q13 (OMIM 114500)
gain Xp22.13 Xp22.11 SCML1 ARX  
gain Xp11.22 Xp11.1 Hs.3383.1 Hs.224455  
gain Xq24 Xq26.3 FLJ32122 CXX1  
  1. These are condensed results of the ChARM analyses: overlapping regions with evidence for up- or down-regulation from various analyses of different cross-correlation window sizes have been fused into single regions. The original ChARM output including p values for each region and additional annotation can be found in Additional file 1. Hereditary colorectal cancer syndromes are indicated along with their OMIM ID. Gene symbols are official or provisional HUGO symbols if available, otherwise names of Unigene clusters. Information about known tumor genes in misregulated regions were extracted from the literature. Tumor-associated genes are located within expression islands or in near vicinity.